Standard fit report for fits of SISCA to HG_Herring data.
Data Scenario: setup_HG
Model Hypothesis: setup_Aggregate_AR1comps
Species:
Stocks:
Max Gradient: 0.0019872
Objective Function value: 166.1804007
Time to fit model: 0.06
PD Hessian: FALSE
No. of Non-finite SEs: 1
Figure 1: Time series of spawning biomass with scaled spawn indices (top), recruitments (second row), natural mortality (third row), and harvest rates (bottom row) for substocks of HG_Herring. Stocks are, from left to right,Aggregate.
Figure 2: Model fits to spawn indices.
Figure 3: Average model fits to age data. Stocks are left to right, and gears are top to bottom.
Figure 4: Model fits to age data, averaged over stock and time. Gears are top to bottom.
| \(\tau^{age}_{Red}\) | \(\tau^{age}_{SR}\) | \(\tau^{age}_{Gn}\) | \(\tau^{surv}_{Su}\) | \(\tau^{surv}_{D}\) | |
|---|---|---|---|---|---|
| Aggregate | 0.476 | 0.441 | 0.646 | 0.483 | 0.475 |
Figure 5: Age-1 recruitments for all stocks. Equilibrium unfished recruitment \(R_0\) is indicated by the horizontal dashed line. Second row shows recruitment residuals on the log scale, with the average of estimated residuals shown by the horizontal red dashed line.
Figure 6: Stock-recruit curves (solid lines) and modeled recruitments (coloured points)
Figure 7: Catch in biomass units for each stock (rows). Stacked bars show the total yearly catch for each commercial fleet, and the dead ponded fish shown with a red border.
Figure 8: Catch in biomass units for each stock (rows). Stacked bars show the total yearly catch for each commercial fleet, and the dead ponded fish shown with a red border.
Figure 9: Selectivity-at-age for each fleet (rows). Aggregate stock average selectivity curves are shown as thick grey lines, while sub-stock specific estimates are shown as dashed thin coloured lines.
Figure 10: Equilibrium yield curves as a function of fishing mortality rates, assuming all fishing mortality comes from the gillnet fleet.
Figure 11: Model fits to yearly Aggregate stock age compositions for the reduction fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 12: Model fits to yearly Aggregate stock age compositions for the seineRoe fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 13: Model fits to yearly Aggregate stock age compositions for the gillnet fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 14: Age composition residuals for the Aggregate sub-stock. Positive residuals are black black, while negative residuals are red.
Figure 15: Model fits to tail compressed yearly Aggregate stock age compositions for the reduction fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 16: Model fits to tail compressed yearly Aggregate stock age compositions for the seineRoe fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 17: Model fits to tail compressed yearly Aggregate stock age compositions for the gillnet fleet. Grey bars are age composition observations, and lines/points are the model expected values.
| objFun | obsSurface | obsDive | ageRed | ageSR | ageGill | |
|---|---|---|---|---|---|---|
| Total | 166.18 | -8.2 | -6.57 | -0.47 | -22.88 | 7.28 |
| Aggregate | 166.18 | -8.2 | -6.57 | -0.47 | -22.88 | 7.28 |
| V1 | |
|---|---|
| objFun | 166.180000 |
| recDevs | 87.960000 |
| initDevs | 10.390000 |
| h | 7.950000 |
| M | 0.280000 |
| tvMdev | 66.600000 |
| IGtau_surf | -4.220000 |
| IGtau_dive | -4.190000 |
| tvSelAlpha | 0.000000 |
| tvSelBeta | 0.000000 |
| selAlphaRed | 3.470000 |
| selAlphaSR | 3.470000 |
| selAlphaGn | -0.690000 |
| selBetaRed | -1.360000 |
| selBetaSR | -1.360000 |
| selBetaGn | -0.450000 |
| lnB0 | 3.033368 |
| lnRinit | 5.579506 |
| psiSOK | -20.350000 |
| V1 | |
|---|---|
| objFun | 166.18 |
| MDev | 0.92 |
| hDev | 0.92 |
| selAlphaDevR | 0.92 |
| selAlphaDevSR | 0.92 |
| selAlphaDevGn | 0.92 |
| selBetaDevR | 0.92 |
| selBetaDevSR | 0.92 |
| selBetaDevGn | 0.92 |
| phase | objFun | maxGrad | nPar | convCode | convMsg | time |
|---|---|---|---|---|---|---|
| 1 | 545.6249 | 0.0000657 | 3 | 0 | relative convergence (4) | 0.0067167 |
| 2 | 544.5749 | 0.0000884 | 13 | 0 | relative convergence (4) | 0.0042500 |
| 3 | 472.7940 | 0.0000726 | 81 | 0 | relative convergence (4) | 0.0044667 |
| 4 | 266.2927 | 0.0001493 | 146 | 0 | relative convergence (4) | 0.0066167 |
| 5 | 266.2927 | 0.0000750 | 146 | 0 | relative convergence (4) | 0.0042000 |
| 6 | 260.4157 | 0.0012926 | 150 | 0 | relative convergence (4) | 0.0067000 |
| 7 | 258.5197 | 0.0005931 | 153 | 0 | relative convergence (4) | 0.0074500 |
| 8 | 166.2809 | 0.0010105 | 154 | 0 | relative convergence (4) | 0.0094000 |
| 9 | 166.1804 | 0.0019872 | 155 | 0 | relative convergence (4) | 0.0075333 |
| RE | NA | NA | NA | NA | NA | NA |
| est | se | gr | cv | |
|---|---|---|---|---|
| lnB0_p | 3.0334 | NaN | -0.0039 | NaN |
| lnRinit_p | 5.5795 | 0.4453 | -0.00024 | 0.0798 |
| logit_ySteepness | 0.7000 | 0.6327 | 7.1e-05 | 0.9038 |
| lnM | -1.0985 | 0.2245 | 0.0016 | 0.2044 |
| fDevs_ap | 0.5869 | 0.4777 | -4.8e-05 | 0.814 |
| fDevs_ap.1 | -0.2052 | 0.5021 | -4.4e-05 | 2.4466 |
| fDevs_ap.2 | 0.3640 | 0.4819 | -3.5e-05 | 1.324 |
| fDevs_ap.3 | 1.1545 | 0.4634 | -4.9e-05 | 0.4014 |
| fDevs_ap.4 | -0.0716 | 0.5191 | -1.3e-05 | 7.2519 |
| fDevs_ap.5 | 0.3051 | 0.5165 | -6.7e-06 | 1.6929 |
| fDevs_ap.6 | -0.5053 | 0.8006 | -3.3e-06 | 1.5845 |
| fDevs_ap.7 | -0.3259 | 0.8673 | -2.4e-06 | 2.6616 |
| fDevs_ap.8 | -0.2019 | 0.9162 | -1.7e-06 | 4.5384 |
| fDevs_ap.9 | -0.2406 | 0.9014 | -2.5e-06 | 3.7461 |
| lnSelAlpha_g | 0.9967 | 0.0544 | 0.00087 | 0.0546 |
| lnSelAlpha_g.1 | 1.3465 | 0.0432 | 0.0022 | 0.0321 |
| lnSelAlpha_g.2 | 1.6508 | 0.0433 | -0.016 | 0.0262 |
| lnSelBeta_g | 0.6738 | 0.0934 | 0.00021 | 0.1386 |
| lnSelBeta_g.1 | 0.6011 | 0.0734 | 3e-05 | 0.1221 |
| lnSelBeta_g.2 | 0.2678 | 0.1148 | 0.0061 | 0.4289 |
| lntau2Obs_pg | -1.4550 | 0.1995 | 6.1e-05 | 0.1371 |
| lntau2Obs_pg.1 | -1.4886 | 0.2048 | -3.3e-05 | 0.1376 |
| recDevs_vec | 2.3259 | 0.2519 | -0.00046 | 0.1083 |
| recDevs_vec.1 | 0.3123 | 0.3144 | -8.1e-05 | 1.0066 |
| recDevs_vec.2 | -0.0995 | 0.3144 | 3.8e-06 | 3.1599 |
| recDevs_vec.3 | -0.2897 | 0.2824 | -0.00013 | 0.975 |
| recDevs_vec.4 | -0.4131 | 0.2932 | -5.8e-05 | 0.7098 |
| recDevs_vec.5 | 1.3815 | 0.2695 | -0.00024 | 0.1951 |
| recDevs_vec.6 | 0.0337 | 0.6519 | -4.6e-05 | 19.3392 |
| recDevs_vec.7 | 0.8776 | 0.4813 | -0.00021 | 0.5484 |
| recDevs_vec.8 | 0.8650 | 0.4245 | -0.00026 | 0.4907 |
| recDevs_vec.9 | 0.8925 | 0.4271 | -3e-04 | 0.4785 |
| recDevs_vec.10 | 0.5940 | 0.5341 | -0.00028 | 0.8992 |
| recDevs_vec.11 | 1.2785 | 0.4167 | -4e-04 | 0.3259 |
| recDevs_vec.12 | -0.8615 | 0.7473 | -2e-05 | 0.8674 |
| recDevs_vec.13 | -1.4533 | 0.6842 | -1e-05 | 0.4708 |
| recDevs_vec.14 | -1.2052 | 0.6833 | -1.2e-05 | 0.567 |
| recDevs_vec.15 | -0.4194 | 0.5200 | -3e-05 | 1.2398 |
| recDevs_vec.16 | 0.0129 | 0.5155 | -3.1e-05 | 40.0259 |
| recDevs_vec.17 | 0.6841 | 0.3910 | -9.7e-05 | 0.5715 |
| recDevs_vec.18 | 0.5262 | 0.3324 | -8.9e-05 | 0.6318 |
| recDevs_vec.19 | 1.2485 | 0.2570 | -0.00024 | 0.2058 |
| recDevs_vec.20 | 1.1412 | 0.2552 | -0.00042 | 0.2236 |
| recDevs_vec.21 | 1.2517 | 0.2469 | -0.00068 | 0.1972 |
| recDevs_vec.22 | -0.3393 | 0.3017 | 0.002 | 0.8892 |
| recDevs_vec.23 | -0.1813 | 0.3206 | -0.0019 | 1.7689 |
| recDevs_vec.24 | 0.2879 | 0.3132 | 0.00061 | 1.0882 |
| recDevs_vec.25 | -0.2763 | 0.3117 | -7e-05 | 1.1283 |
| recDevs_vec.26 | 2.8017 | 0.2727 | 0.0017 | 0.0974 |
| recDevs_vec.27 | 0.5840 | 0.2766 | -4.5e-05 | 0.4735 |
| recDevs_vec.28 | -0.4973 | 0.2831 | 0.00022 | 0.5692 |
| recDevs_vec.29 | -0.7079 | 0.2884 | -0.00025 | 0.4075 |
| recDevs_vec.30 | 1.3470 | 0.2697 | -0.00086 | 0.2002 |
| recDevs_vec.31 | 0.5006 | 0.2717 | -0.00054 | 0.5428 |
| recDevs_vec.32 | -1.0913 | 0.3029 | -0.00059 | 0.2775 |
| recDevs_vec.33 | -0.6847 | 0.2637 | -0.00027 | 0.3852 |
| recDevs_vec.34 | 1.6869 | 0.2336 | -0.00057 | 0.1385 |
| recDevs_vec.35 | 0.6303 | 0.2365 | 0.00098 | 0.3752 |
| recDevs_vec.36 | -0.2612 | 0.2460 | 0.00029 | 0.9418 |
| recDevs_vec.37 | -1.3080 | 0.2805 | 5.5e-05 | 0.2144 |
| recDevs_vec.38 | 0.7195 | 0.2570 | -4.9e-05 | 0.3572 |
| recDevs_vec.39 | -1.8275 | 0.3590 | 2.8e-06 | 0.1964 |
| recDevs_vec.40 | -1.8827 | 0.3675 | -0.00027 | 0.1952 |
| recDevs_vec.41 | -1.0431 | 0.3474 | -0.00019 | 0.333 |
| recDevs_vec.42 | 0.2066 | 0.2801 | -0.00019 | 1.3559 |
| recDevs_vec.43 | 0.4638 | 0.2750 | -4.2e-08 | 0.5929 |
| recDevs_vec.44 | 1.5501 | 0.2453 | 5e-04 | 0.1582 |
| recDevs_vec.45 | -1.6222 | 0.3081 | -4e-05 | 0.1899 |
| recDevs_vec.46 | -0.4206 | 0.2942 | -6e-05 | 0.6994 |
| recDevs_vec.47 | -0.4245 | 0.3024 | 9e-05 | 0.7123 |
| recDevs_vec.48 | -0.2809 | 0.3026 | -1.3e-06 | 1.0771 |
| recDevs_vec.49 | 0.8457 | 0.2849 | -2.6e-05 | 0.3369 |
| recDevs_vec.50 | -0.7796 | 0.4085 | -1.3e-05 | 0.5239 |
| recDevs_vec.51 | 0.5261 | 0.3649 | 1.4e-06 | 0.6936 |
| recDevs_vec.52 | -0.7901 | 0.4461 | -1.2e-05 | 0.5646 |
| recDevs_vec.53 | 0.7609 | 0.3792 | -7.5e-06 | 0.4984 |
| recDevs_vec.54 | -0.8982 | 0.3911 | -5.8e-05 | 0.4355 |
| recDevs_vec.55 | 0.8317 | 0.3401 | 1.5e-05 | 0.4089 |
| recDevs_vec.56 | -1.1114 | 0.4217 | -1.4e-05 | 0.3794 |
| recDevs_vec.57 | 0.3725 | 0.3490 | 1.4e-05 | 0.9369 |
| recDevs_vec.58 | -0.2121 | 0.3706 | 4.2e-07 | 1.7475 |
| recDevs_vec.59 | 1.3819 | 0.3100 | 1.8e-05 | 0.2243 |
| recDevs_vec.60 | -0.6795 | 0.3839 | -1.4e-05 | 0.565 |
| recDevs_vec.61 | -0.1432 | 0.3649 | -2e-06 | 2.5481 |
| omegaM_pt | -0.1803 | 0.9778 | 0.00016 | 5.4231 |
| omegaM_pt.1 | -0.1620 | 0.9772 | 0.00016 | 6.031 |
| omegaM_pt.2 | -0.0404 | 0.9751 | 0.00015 | 24.1497 |
| omegaM_pt.3 | 0.0750 | 0.9731 | 0.00013 | 12.9753 |
| omegaM_pt.4 | 0.2412 | 0.9687 | 0.00011 | 4.0161 |
| omegaM_pt.5 | 0.5365 | 0.9624 | 9.5e-05 | 1.7938 |
| omegaM_pt.6 | 0.4763 | 0.9605 | 9.3e-05 | 2.0168 |
| omegaM_pt.7 | 0.3337 | 0.9613 | 8.7e-05 | 2.8809 |
| omegaM_pt.8 | 0.3522 | 0.9629 | 8.6e-05 | 2.734 |
| omegaM_pt.9 | 0.2884 | 0.9647 | 7.7e-05 | 3.3453 |
| omegaM_pt.10 | 0.2451 | 0.9655 | 5.6e-05 | 3.9384 |
| omegaM_pt.11 | 0.2346 | 0.9633 | 2.3e-05 | 4.1065 |
| omegaM_pt.12 | 0.3670 | 0.9581 | -1.9e-05 | 2.6104 |
| omegaM_pt.13 | 0.5924 | 0.9534 | -7e-05 | 1.6094 |
| omegaM_pt.14 | 0.7305 | 0.9547 | -9.7e-05 | 1.3069 |
| omegaM_pt.15 | 0.4189 | 0.9635 | -8.7e-05 | 2.3001 |
| omegaM_pt.16 | -0.0082 | 0.9678 | -7.9e-05 | 118.3521 |
| omegaM_pt.17 | -0.2381 | 0.9663 | -7.2e-05 | 4.0582 |
| omegaM_pt.18 | -0.2798 | 0.9610 | -6.6e-05 | 3.4346 |
| omegaM_pt.19 | -0.2404 | 0.9576 | -6.5e-05 | 3.9825 |
| omegaM_pt.20 | -0.2629 | 0.9569 | -6.8e-05 | 3.6403 |
| omegaM_pt.21 | -0.3927 | 0.9550 | -8.2e-05 | 2.4318 |
| omegaM_pt.22 | -0.4338 | 0.9502 | -0.00012 | 2.1903 |
| omegaM_pt.23 | -0.2809 | 0.9447 | -0.00018 | 3.3628 |
| omegaM_pt.24 | -0.1448 | 0.9412 | -0.00014 | 6.5016 |
| omegaM_pt.25 | 0.0375 | 0.9391 | -0.00019 | 25.0518 |
| omegaM_pt.26 | 0.1970 | 0.9379 | -0.00021 | 4.7598 |
| omegaM_pt.27 | 0.2428 | 0.9364 | -0.00022 | 3.857 |
| omegaM_pt.28 | 0.2504 | 0.9372 | -0.00014 | 3.7431 |
| omegaM_pt.29 | 0.2998 | 0.9393 | -5.4e-05 | 3.1329 |
| omegaM_pt.30 | 0.3167 | 0.9403 | 3.5e-05 | 2.969 |
| omegaM_pt.31 | 0.3734 | 0.9394 | 0.00011 | 2.5159 |
| omegaM_pt.32 | 0.4609 | 0.9379 | 0.00013 | 2.0349 |
| omegaM_pt.33 | 0.5077 | 0.9373 | 0.00012 | 1.846 |
| omegaM_pt.34 | 0.3646 | 0.9366 | 6.7e-05 | 2.5686 |
| omegaM_pt.35 | 0.0522 | 0.9370 | -1.1e-05 | 17.959 |
| omegaM_pt.36 | -0.0266 | 0.9358 | -0.00013 | 35.1357 |
| omegaM_pt.37 | -0.1006 | 0.9350 | -0.00018 | 9.2915 |
| omegaM_pt.38 | 0.1091 | 0.9293 | -0.00021 | 8.5152 |
| omegaM_pt.39 | 0.3300 | 0.9233 | -0.00022 | 2.7976 |
| omegaM_pt.40 | 0.4544 | 0.9251 | -0.00022 | 2.0359 |
| omegaM_pt.41 | 0.4360 | 0.9269 | -0.00021 | 2.1259 |
| omegaM_pt.42 | 0.4004 | 0.9250 | -0.00021 | 2.3103 |
| omegaM_pt.43 | 0.4012 | 0.9256 | -0.00023 | 2.3068 |
| omegaM_pt.44 | 0.1728 | 0.9281 | -0.00027 | 5.3716 |
| omegaM_pt.45 | 0.1155 | 0.9277 | -0.00031 | 8.0322 |
| omegaM_pt.46 | 0.3162 | 0.9232 | -0.00031 | 2.9199 |
| omegaM_pt.47 | 0.5047 | 0.9181 | -0.00032 | 1.8191 |
| omegaM_pt.48 | 0.5565 | 0.9134 | -0.00032 | 1.6414 |
| omegaM_pt.49 | 0.5682 | 0.9144 | -3e-04 | 1.6094 |
| omegaM_pt.50 | 0.5186 | 0.9237 | -0.00028 | 1.7812 |
| omegaM_pt.51 | 0.0801 | 0.9259 | -0.00026 | 11.5609 |
| omegaM_pt.52 | -0.0413 | 0.9264 | -0.00025 | 22.4401 |
| omegaM_pt.53 | -0.1742 | 0.9253 | -0.00023 | 5.3131 |
| omegaM_pt.54 | -0.4433 | 0.9277 | -0.00022 | 2.0931 |
| omegaM_pt.55 | -0.4118 | 0.9267 | -2e-04 | 2.2502 |
| omegaM_pt.56 | -0.3699 | 0.9278 | -0.00019 | 2.5084 |
| omegaM_pt.57 | -0.3305 | 0.9279 | -0.00018 | 2.8077 |
| omegaM_pt.58 | -0.2257 | 0.9276 | -0.00017 | 4.1107 |
| omegaM_pt.59 | -0.1379 | 0.9260 | -0.00016 | 6.7131 |
| omegaM_pt.60 | -0.0446 | 0.9244 | -0.00014 | 20.7453 |
| omegaM_pt.61 | 0.2067 | 0.9231 | -0.00013 | 4.4664 |
| omegaM_pt.62 | 0.4670 | 0.9241 | -0.00011 | 1.9787 |
| omegaM_pt.63 | 0.7966 | 0.9185 | -9.8e-05 | 1.153 |
| omegaM_pt.64 | 0.5271 | 0.9308 | -7.9e-05 | 1.7657 |
| omegaM_pt.65 | -0.0164 | 0.9444 | -5.9e-05 | 57.5531 |
| omegaM_pt.66 | -0.2331 | 0.9654 | -3.8e-05 | 4.1407 |
| omegaM_pt.67 | -0.2387 | 0.9818 | -1.8e-05 | 4.1135 |
| logitphi1_g | 0.6199 | 0.5531 | 2.7e-06 | 0.8921 |
| logitphi1_g.1 | 0.5844 | 0.2425 | 2e-05 | 0.415 |
| logitphi1_g.2 | 0.6909 | 0.4435 | -0.0059 | 0.6419 |
## Not Yet Implemented
Figure 18: Estimated correlation matrices for age composition residuals in the reduction fleet. The circles above the visualise the numbers below the diagonal.
Figure 19: Estimated correlation matrices for age composition residuals in the seineRoe fleet. The circles above the visualise the numbers below the diagonal.
Figure 20: Estimated correlation matrices for age composition residuals in the gillnet fleet. The circles above the visualise the numbers below the diagonal.
Figure 21: Diagnostic plot for compositional likelihood function.
Figure 22: Plots of average age composition fits at the major stock level. Left is SISCA, right is ISCAM.
Figure 23: Comparison of spawning stock biomass and age-2 recruitment at the major stock level between ISCAM and SISCA.